Deep Shadow Condition
by RyuuenLu
Summary: HYDRA has finally decided to step out of the shadows and there is only one thing to do. However, are they ready for their once life to come to an end. Part 2 of The S.H.I.E.L.D Protocols.
1. Here we go again

**_AN: Hello everyone, I'm back. A little bit later than I had expected, however, summer is summer so. For those who are new, I recomamd you to read Quake Protocol before reading this, otherwise this one will just be confusing. I have also created an Insta where you can follow the progres on this story and other projects im working on. you find me under the name RyuuenLu Now, happy reading!_**

 _All rights goes to Marvel!_

Daisy Johnson POV

Looking at the door in front of me I took a deep breath, closing my eyes at the progress. I still had a hard time trying to understand how I have even ended up standing in front of the door to Coulson's office. One minute I had been talking to Pepper, mostly because Natasha had not answered her phone. Somewhere in the mix she had managed to convince me to talk to Coulson, how that woman managed to make people do things they do not want to do is still a mystery.

Taking one more deep breath I lift my hand to knock on the door. "It's open!" Coulson called out after I gave the door a small knock. Carefully looking in to the room, I could see how Coulson was working on a pile of paperwork. "Do you have a minute?" I asked carefully, and I could see how Coulson looked up in surprise when he heard my voice. With a nod of his head I entered the office, carefully closing the door behind me as I did. "What can I do for you?" Coulson asked as he put down the paper that he was reading.

"Well, I was on the phone with Pepper and before I knew what happened she had managed to convince me to talk to you." I told him, I could not help but to bite my lower lip out of worry. It has been around two months since the arrest of one John Garrett, two months since I had blacked out and two very long month of being stuck on the BUS without any type of field work or anything. The first few days had been mostly being laying on a hospital bed, having May, Fitz and the rest of the Avengers with Pepper hanging around to make sure I was okay.

Once back on the BUS once more, Simmons had made sure I had had everything I needed. It had taken her a few days to get over everything. However, with a long talk with Fitz she had gotten over the fact that I had been lying to her and Coulson this whole time. It had been easier for Trip to fit in to the group. He had after all not been along during the whole betraying the team in the first place. Coulson on the other hand had not said a single word to me since the arrest of Garrett and I'm very sure May had not talked to him either. "Well, it would not be the first time Pepper managed to do something like that." Coulson pointed out, pulling me back into reality.

"I thought she only had that power on people when they were in the same room." I answered, smiling a little at that. "Well, If it's not Tony." I then quickly added, and Coulson smiled at that. "I have said it before that we should send Pepper into the front line, most of the fights that team ends up in would be over within five minutes." Coulson commented, and I could not help but to laugh. Some of the tension in my body was starting to grow smaller and I sat down on the chair that was in front of the desk. "I guess it's for our best that we talked about what has happened." I then pointed out and I could see how the smile Coulson have had was gone.

"There isn't much to talk about Skye." He said, turning his attention back to the paperwork once more. "Daisy." I told him, crossing my arms as I did. "Right, Daisy." Coulson said, and I could not help but to roll my eyes. "You never had a problem with calling me Daisy before." I pointed out and the look I got from Coulson said more than anything else in that moment. "Look, I had too! Don't you think I never looked in to what you guys were doing once I got to the tower." I pointed out, my eyes narrowed now.

"Fury told me you had called in that I had gone missing, he also told me you had been very angry about it. Not to mention all your tries to find me and the length you have gone. I saw how you reacted to when Simmons saw me and how you were acting after that." I continued to tell him. "Then let's not forget about your behaviour after we found you!" I finally added, this comment made Coulson freeze up a little. "So, you were there! This whole time you had me think I was going crazy!" He half called out and I looked down. "I'm sorry about that, it was not in any of my plans that you were going to be taken. If it should have been anyone to be taken away that day it should have been me!" I told him, closing my eyes only to see that moment once more.

The room fell into a long silence at that, I kept my eyes closed alongside taking a few deep breaths. "You are also the mysterious daughter I never knew Melinda had." Coulson then pointed out and I could not help the smile that started to grow on my lips at that. "Yeah, she sorts of adopted me right before Christmas. I think she did it long before that. However, being who she is she never told anyone until the right moment." I told him, opening my eyes once more. "And…" Coulson than started to say, only to struggle to come up with the right way of asking the question he wanted to have an answer too.

"It's you, have always been. Since the moment I stepped my foot on this BUS the first time all those months ago, even if you have acted like an ass." I answered the question he had tried to ask. "To my defence I didn't know! So, part of this is your own fault!" Coulson pointed out and I rolled my eyes. "Well I was going to tell you before everything went downhill." I told him, and Coulson lift one eyebrow at that. "When?" He asked out of surprise. "May and I were talking about it the night you found us sitting out on the couch. We were talking about telling you everything. However, things did change quite fast after you showed up." I told him, shame was starting to show in his eyes this time.

"I'm sorry about that." Coulson said, and I just waved my hand at that. "How about we just call it even and try to work things out together from now on." I asked him, and Coulson nodded his head at that. "Deal." He said, and I smiled, feeling a little better after it all. I could see how Coulson was about to add something else to it all when suddenly there was an alarm going through the BUS. I could see how Coulson looked up at surprise and my own eyes grow big when I realized what the warning was about. "No! No, no, no!" I started to say before flying out of the chair and head for the door.

"Skye?" I could hear how Coulson called after me, ignoring him I head down to the control room. I could hear how Coulson was coming after me and I could see how the rest of the team was also moving towards the command centre. "Move!" I told Trip, pushing him out of the way. "What is going on?" I could hear May ask once she entered the command centre. "Daisy!" Maria's voice suddenly said and a second later she showed up on the big screen. "Maria! Please tell me it hasn't happened!" I told her and the look in Maria's eyes gave away that I would not like the answer.

"I'm sorry Daisy, Deep Shadow Condition has been activated." Maria told me, and I could not help but to curse quietly under my breath. "Just get there, now! I will pick up the others and we will meet you there!" I told her and pulled out my phone, looking up at Maria once more. "And Maria, be careful." I told her, and Maria nodded her head. "You too Daisy." She answered before the screen went dark once more and the alarm died down. "What is going on?" It was Coulson's time to ask that question and I looked towards him and the rest of the team.

"I will explain everything once we are all in a safe location and when everyone is there. I do not want to go over everything twice." I told him before looking directly towards May. "Could you take us to the tower?" I asked her, and May nodded her head and heads out from the room. Looking down at my phone I took a deep breath. "Time to make a call to Pepper, again." I then said with a heavy sigh and I could see how Coulson was smiling at that. "Not a single word AC!" I told him before making the call. "A second time in one day, what can I do for you Daisy?" Pepper answered, and I could not help but to roll my eyes.

"Take out the emergency bags and grab what is important. We will be at the tower as soon as we can." I only told her, and I could hear how Pepper finished the call before I even got an answer back from her.


	2. Not a chance pirate

_**AN: Second chapter of Deep Shadow Condition, as I was going throthrough my papers for the stories I realised that this part of the series (that now goes under the name of The S.H.I.E.L.D Protocols) will be a bit shorter than I had first thought. However, the third part has already been started on so the wait will not be so long. So for now, chapter 2 out 6!**_

 _All rights goes to Marvel_

 _Daisy Johnson POV_

"Strap in, we will be landing at the Tower in just a few minutes." May said through the com system, something she didn't really had to do since we all had ended up on the couches anyway. "Once we land I think it's best if we just get the others on board and head out once more." I told them all, not that anyone was complaining over that plan at the moment. I knew there was going to be at least one person that will be complaining about all of this. Feeling how we got down for landing I rose up from my seat and headed for the cargo hold, landing on the ground I could see how Tony, Pepper, Bruce and Clint were already walking onboard with their things.

"Where is Natasha and Steve?" I asked as I come to a stop. "Better question is, what is going on?" Tony asked, ignoring him I looked at Clint. "They are on some kind of mission that Fury sent them on." Clint explained. "Shit!" Was the only thing I could say before I took a deep breath. "Alright, everyone up to the common room. Coulson, Fitz, Simmons and Trip are already there. I need to give May the co-ordinates for where we need to head next." I told them all, turning around once more. "Stop! First I want to know what is going on!" Tony called out and I stopped.

"When we are all in a secure place and everyone is there, I will tell you everything. Until then, strap in and be ready for anything." I told him and started to walk up the stairs once more. Stopping outside out of the cockpit, opening the door I could see that May had turned around in the seat and looked at me. "Where to now?" She asked, and I walked over to sit down in the co-pilot seat, handing her a paper with the coordinates. "This seems to be in the middle of nowhere." May pointed out as she puts them in to the system.

"That is one of the points." I told her, pulling on the headphones and May nodded her head. We were up in the air within a few minutes. "I talked to Coulson before all of this started." I told her, making May look over at me. "Pepper made me do it." I told her, and May rolled her eyes. "Let's just get this part over with and we can look in to what the talk to Coulson have made after words." She said I nod my head. "Sounds like a good plan." I answered.

 _-X-X-X-X-X-X-_

"Where are we?" Tony asked, and I could see how he was turning around while he was walking. "A safe place." I answered as I walked towards the gigantic metal door. "Not a chance pirate." I said, putting my hand beside the door and a few seconds later the door starts to open. "If you ever tell Fury my code I will make sure that every single black mail I have on you will end up on the internet." I told the group behind me before I started to walk into the long tunnel, the lights turning on the deeper in I got. I heard how the others were following me and I entered the meeting room. "Alright, we are in the safe place. Now tell us what is going on." Tony demanded, and I sat down at the table.

"It's still a no Tony, I will not go over everything more than once. Besides, I will need both Maria and Fury here to be able to explain everything right." I told him with a heavy sigh. "So, what, we wait?" Tony asked, and I nodded my head at that. "Just sit down and wait, with any luck Maria and Fury will be here soon so." I then added, this made the rest of the team join me around the big table. A silence fell over them all as they waited, half way in Trip pulls out a deck and a round of poker started within seconds.

Looking at the two teams playing I could not help but to smile just a little at it all, leaning back in my seat I pulled out my phone to check on the time. That's when the security alarm set of and I was quickly on my feet, a long side half of the agents around the table. "What now?" I could hear Fitz say as I started to head for the corridor once more. Hearing how the others were following I slowed down a little, soon reaching the door that we had all entered. Once the two team was standing behind me I could see how the door was opening

My eyes grow big when they landed on Maria and the three doctors that were pushing the hospital bed where Nick Fury was laying on. "What happened?" I asked as I quickly moved towards them to help. "He was shoot, Steve was there when it happened and according to him Fury had already been badly hurt when he showed up." Maria answered me, and I looked at her. "Where is Steve and Natasha?" I asked her eyes narrowed, and Maria lets her head fall a little. "They are missing at the moment." She answered, and I rolled my eyes.

"No one is really missing." I answered her, this time looking down at Fury. "Fury?" Coulson said as we moved passed the teams. "What is going on here!" Clint asked, and he looked at me and Maria with narrowed eyes. "That will have to wait for now." Maria told Clint, turning her head towards the doctors she had come with. "Take him down to the med bay as quickly as possible." She told them, with a nod of their heads they took Fury and head away. "I need you to locate Natasha and Steve, time is starting to run out and the faster we can get to them the better it will be for everyone." Maria then told me, and I nod my head.

"On it!" I told her, turning around I headed for the room we had all been waiting in before. "Daisy, have you made sure there is transportation in this place?" Maria than asked and I looked over my shoulder. "I thought you were in charge of that!" I told her, coming to a stop. Seeing how Maria's eyes grow big in worry I could not help but to smile big and turning around once more. "Don't worry Agent Hill! I have everything under control!" I told her with a laughter as I entered the room.

"May, gear up! I will need to have someone to drive, and I do not wish to be left alone with her!" I could hear Maria call out and I just rolled my eyes. Sitting down in front of the computer Steve had once given me I cast myself right into the work I had been given. There was no way I would let anything happen to Natasha and Steve if there was anything I could do to stop it.


	3. A rescue from fake SHIELD agents

_All rights goes to Marvel_

 _Daisy Johnson POV_

"We need to get a doctor here." The unknown man pointed out and I glanced towards Natasha, I could see how she was in pain but at the same time she tried to hide it. "If we don't put pressure on that wound she's going to bleed out here in the truck." The man then added, and I could see how Maria started to pull out the electric road we had have with us and points it towards the unknown man. Smiling to myself under the mask I was wearing I quickly pulled out my own electric road and put it into the side of the guard sitting beside me, easily putting him out. Seeing that Maria put away her road the both of us started to take of the helmets we had on.

"Ah. That thing was squeezing my brain." Maria commented once her mask was off. "Tell me about it." I told her as I lowered my own and I could feel how both Natasha and Steve looked at both me and Maria out of surprise. My own eyes on the other hand landed on the unknown man sitting beside Natasha. "ho is this guy?" I ask, looking between Natasha and Steve this time. Before either of them had a chance to answer the question. However, the car was coming to a stop and I quickly looked towards Maria. "That question can wait, Maria please get us out of here." I told her, and Maria nods her head, pulling out the Mouse Hole device Fitz had created.

She created a whole in the floor of the van and in the ground below once she was on it. "Everyone get down now!" She ordered once the hole was created, she herself was the first one to jump down. I could see how Steve looked towards the unknown man and nodded his head before he jumped down the holes, the unknown man in question swallows hard before he jumps after. "Can you make it?" I asked Natasha in a low voice and the red head only nodded her head before she jumped after. Taking a deep breath, I jumped after, landing swiftly beside Natasha and looked up at the group in front of me. "Come on, our getaway car is this way!" Maria told us as she started to head down the corridor and we all followed her.

The only sound that could be heard down in the tunnel was the sound of our own feet as we walked, I cast a quick look over my shoulder every now and then to make sure no HYDRA agents were following us. "We are here." Maria said after we had walked for 10 minutes and she stepped up to a metal door and pushed it open, letting sunlight into the darkness that had been around us.

"About time you guys showed up!" I could hear May comment. However, do to the sudden sunlight we all had a hard time seeing. Once my eyes had gotten use the bright light I could see how May was leaning towards the small van. "You guys have been seeing better days." She then added, and I could not help but to roll my eyes. "Watch it!" Natasha told her, and I could see that her eyes were narrowed as she looked towards May who just smiled. "Can we just get out of here?" I asked, opening the back door and jumped inside. Natasha followed me and sat down beside me as Steve and the still unknown man took the seats in front of us.

Maria took the codriver seat and May took the driver seat, once she was seated she started up the car and headed towards the bunker that had now turned into our hiding spot. "So, I never got an answer out of you?" I pointed out after a few minutes of silence, I leaned forward so that I was able to look at the unknown man. "Who are you?" I asked once more at the surprised look that had shown up on his face. "Sam Wilson." He answered me, and I nodded my head at that.

"Tell me Mr. Sam Wilson, how did you end up with these two lunatics?" I asked him, my eyes narrowed a little and my voice serious. "Oi!" I could hear Natasha point out before she slaps my head. "Ouch!" I complained, turning around to look at Natasha I started to rub the spot where she had hit me. "That really hurt you know!" I told her, my eyes narrowed as I looked at the woman. "You deserved it." Natasha told me, her own eyes narrowed as she looked at me.

"Enough!" May told the two of us before I had a chance to answer Natasha back and both of us lowered our heads. "Yes Mel/ Yes mom." The two of us said at the same time and I could see how Sam sent Steve a confused look. "Daisy Johnson aka Quake. She is an Avenger like me and Natasha." Steve started to explain and he nodded his head towards me. "Melinda May, Daisy's adopted mother and a S.H.I.E.L.D agent." He then continued to say and nodded his head towards May this time.

"Got it." Sam answered with nod of his head, it being clear that he was still being confused over it all. "How long until we reach the safe point?" Maria asked, and I could see how May looked towards her. "We are two hours away, I can try to shorten that." May answered, with a glance towards Natasha I could see that the pain was finally taking over. "Try to make it half that time." I told her, and May nodded her head and silence fell between us all after that.

 _-X-X-X-X-X-X-X-_

May parked the car just in front of the steel doors that would lead down to the bunker we now called our HQ. Jumping out of the van I carefully helped Natasha out to. Steve and Sam join us, and Maria walked directly over to the door and opened it up. One after one we entered the bunker only to be greeted by Coulson and Clint. "You guys have seen better days." Clint pointed out and I could feel the urge to hit him from Natasha. "That's what I said." May simply told him, making Clint smile big.

"We should get her to the doctor." Coulson commented, his eyes on Natasha and I nodded my head in agreement to that. "They might, however want to see him first." Maria pointed out and I took a deep breath. "You just had to remind me, didn't you?" I asked, and Maria nodded her head. "See who?" Natasha asked, and I glanced towards her. "You'll see." I told her before looking towards Steve and Sam.

"You two will come with me." I then told them as I started to lead them down towards the room where we had put Nick in. Walking slowly just to make sure Natasha was alright. However, I could feel how she was tense. We soon reached the room and I carefully pushed the door open and stepped inside. "About damn time." Fury commented when he saw us coming in. "You.Son.Off.A…" Natasha started to say, her voice low and the anger was clear. "I'm agreeing with Natasha on this note." Was the only thing Steve said and I could see him crossing his arms.

"Lacerated spinal column, cracked sternum, shattered collarbone, perforated liver, one hell of a headache." Fury started to explain. "Don't forget your collapsed lung." The doctor pointed out and I could see how Fury rolled his eye. "Oh, let's not forget that. Otherwise, I'm good." Fury added, and I could not help but to shake my head at that. "They cut you open, your heart stopped." Natasha pointed out, the anger had now turned into shock. "Tetrodotoxin B. Slows the pulse to one beat a minute. Banner developed it for stress. Didn't work so great for him, but we found a use for it." Fury explained.

"Why all the secrecy? Why not tell us?" Steve asked. "That's enough for now!" I told them before Fury had a chance to say anything else. "You!" I then added, looking over towards the doctor. "We have a GSW here and she's lost at least a pint." I then told him, and the doctor nodded his head as he walked over to me and Natasha so that he could take over. "You two should find the others, once Natasha is done we will meet you all and finally tell you all what is going on." I then added, looking towards Steve and Sam who nodded their heads. The two of them turned around and walked out and the doctor lead Natasha to another room. "This won't end well. You know that right?" I asked, and Fury nodded his head. "It never does." He answered.


	4. The plan is taking form

_All rights goes to Marvel_

 _Daisy Johnson POV_

Once Natasha had been fixed up by the doctor, I found myself sitting between Fury and Maria. Coulson's team, my own and Sam sat on the other side of the table. "So, an explanation." I started to say before taking a deep breath. "To answer the questions, you asked earlier Steve. The reason why we let you guys think Fury died at the hospital." I started to say, knowing that we had to start somewhere. "Any attempt on the director's life had to look successful." Maria continued, her voice short and to point. "Can't kill you if you're already dead. Besides, I wasn't sure who I could trust within those walls." Fury continued to say.

"In other words, welcome to Deep Shadow Condition." I translated. "If HYDRA were to move away from the shadows we knew they were hiding within, Deep Shadow Condition was to be activated. Basically, it meant that I would take all of you here for safety during the time we figure out our next move. Letting HYDRA think they could take out Fury was a part of the plan I wasn't really happy about at first." I then continued, and I could see a few heads nodding at that. "Now that we are all here, let's go over the next part of the plan." I finished, and Maria took out a picture of Alexander Pierce.

"This man declined the Nobel Peace Prize. He said, 'Peace wasn't an achievement, it was a responsibility.'" Fury started to say, his eye narrowed as he looked at the picture. "See, it's stuff like this that gives me trust issues." He then added, and I could not help but to roll my eyes at his comment. "We have to stop the launch." Natasha pointed out and doing a quick scan around me I could see that Steve and Sam had told Coulson and the others what had happened, since neither of them looked confused. "I don't think the Council's accepting my calls anymore." Fury said as he put a case on the table and open it up, showing of the three chips that were inside.

"What's that?" Sam, Trip and Fitz asked at the same time as they were looking at the chips. "Once the Helicarriers reach three thousand feet, they'll triangulate with Insight satellites becoming fully weaponized." Maria explained. "We need to breach those carriers and replace their targeting blades with our own." Fury continued the explanation. "One or two won't cut it. We need to link all three carriers for this to work, because if even one of those ships remains operational a whole lot of people are going to die." Maria took over saying once more.

"We have to assume everyone aboard those carriers is HYDRA. We need to get pass them, insert the server blades, and maybe, just maybe, we can salvage what's left…" Fury started to say once more only to be stopped by Steve. "We're not salvaging anything." He points out and all eyes were on him. "We're not just taking down the carriers, Nick, we're taking down S.H.I.E.L.D." He then added, and I could feel how my eyes grow big. I had expected a comment like this to happen. However, I never thought it would come out of Steve Rogers mouth.

"S.H.E.I.L.D had nothing to do with it." Fury quickly defends with, his arms crossing over his chest. One look towards Steve and I knew Fury had already lost this fight. "You gave me this mission, this is how it ends. S.H.I.E.L.D's been compromised, you said it yourself. HYDRA grew right under your nose and nobody notice." Steve continued saying. "We did notice, or have you already forgotten Rogers?" I could not help but to say. There was more ice in my voice than I had expected, and it made everyone in the room freeze up themselves.

"Besides, Fury had no idea about Barnes." I then added, my own arms crossed now, and I could see a hint of shame flash in Steve's eyes. "S.H.I.E.L.D, HYDRA, it all goes." Steven than said, letting go of the other part for the time being. "He's right." Maria agreed, this made both me and Fury look at her out of surprise. Fury turned his head to look at everyone else that was sitting around the table. Every single one of them nod their head in agreement. "Don't look at me. I do what he does, just slower." Sam was the only one to answer and Fury turned his head to look at me. "I'm sorry Nick." I told him, knowing fully well that Steve was right.

"Well… Looks like you're giving the orders now, Captain." Fury told Steve who nodded his head. "Damn right I am." He answered, and I rolled my eyes at that. "Alright, now that we got that part out of the way it's time we really do something about it all." I commented and leaned forward on the table. "I thought Cap was the one giving orders." I could hear Sam whisper, only to have Natasha wave her hand at him. "We need to split up in three teams." I then continued, looking at the group in front of me. "Clint, you and Coulson's team will head for the HUB. Make sure Hand has all the help she will need." The group in question nodded their heads at that and I could feel how May was eyeing me carefully.

"Stark, Pepper and Bruce." I then continued and the three in question looked at me. "Make sure there is an army of lawyers waiting for us all once all of this is over." I told them, Tony smiling big at this and nodded. "That is easy fixed." He answered with a grin. Looking towards the rest of the agents in the room I took a deep breath. "That means we will take care of the work on the front line. Natasha, do you mind impersonate a council member?" I then continued, turning my eyes towards Natasha and she nodded her head in an answer. "Good, Maria. For this you are going to have to be our eyes and ears in all of this." I told Maria, even she nodded her head at that. "Just get me inside and I can take care of that." She answered me, and I smiled a little at that.

"Fury, you will stay close by to Natasha at all time. I would recommend, however to do that outside. If this is to work properly we need your eye to unlock and release all information there is about both S.H.I.E.L.D and HYDRA." Looking towards Fury as I spoke the older man nodded his head, still being clear that he wasn't all to happy about this plan. "And for the rest of us?" Sam asked, turning my head towards him I smile. "We will take down a carrier each." I told him, and Sam lowers his head at that. "I was afraid you would say that." He commented, and I rolled my eyes.

"Once the secrets are out and S.H.I.E.L.D is no more, you all need to go into hiding. I will contact you all a week later to give you a location to a safe place where we can meet up and decide from there on what to do." I finished, and heads were being nodded again. "Good, now head out." I told them and stood up. Seeing how both May and Coulson stood up at the same time too I had a strong feeling they were going to try and change the plan. Walking towards one of the hallways I could hear how they followed me, coming to a stop I leaned towards the wall and crossed my arms.

"I will not change my mind." I told the two of them before they even had the chance to say anything. "Skye…" Coulson started to say, and I rolled my eyes. "Daisy." I corrected him, and I could hear how he cursed quietly under his breath. "Daisy, maybe it's better you let Clint do this and you can come with us. Hand would react better if you were with us and Clint has more training when it comes to things like this." Coulson finished of saying and my eyes narrowed in a bit of anger. Opening my mouth to comment on it I remembered that Coulson was still in the dark about one thing and I took a deep breath.

"I will be fine. Besides, I'm trained to do things like this too. Natasha, Maria, Fury and Steve will be there all the way." I told him, only to see that he was not happy over it. "Just be careful. I want to see you before the week in hiding is over." May cut in to say before Coulson had a chance to continue. "The point of us going into hiding is to make sure no one else gets hurt. So, no contact during that week and you know that." I told her, giving her my full attention. I could see that May wasn't happy over any of this. However, she had accepted that there was nothing she could say and do to make me change my mind. "I better hear from you within the week." She warned me as she gave me a hug. "I will, just make sure the rest of the team is safe." I told her, hugging her back.

"I will." Was the only answer I got from her before she released me. Turning my head to the side I could see that Coulson had finally given up and before I knew it he was hugging me, something I did not expect to happen any time soon. "Be careful." He whispered into my ear and I nod my head. "I will." I assured him, and Coulson released me. "I need to take care of a few things, you guys should head out as fast as possible." I told them and the two senior agents, the two people that were the closest thing I had ever had to a mother and father, nodded their heads. They turned around and walked back into the meeting room once more and I took a deep breath.

"I would recommend the Providence once all of this is over." A voice said from behind me and I just rolled my eyes, not surprised that Fury had managed to sneak up on me. "If you say so sir." I answered him, turning around to look at him I could see a small box in his hand and I narrowed my eyes. "Don't even think about it. I do not want to have that thing! That is not what I am." I told him, my eyes narrowed, and my mind set. With that, I walked passed Fury in search for Natasha and Maria.


	5. The fall

**_AN: Hello all, this weeks chapter a little late (well... a lot late). It's been one crazy week, but never late than ever so._**

 _All rights goes to Marvel!_

 _Daisy Johnson POV_

Getting into Triskelion had been easier than I had first thought, it seemed that hanging out with Clint had his odd places in the different bases helped out very well. Me, Maria, Steve and Sam soon found ourselves outside of the door that would take us into Project Insight headquarters. "According to the maps this is it." I told them, looking towards the three I was with, I took a step to the side to let Steve take charge. As Steve knocked on the door the rest of us pulled our guns and the tech that had opened up the door looked at us with horror. "Excuse us." Steve said politely and entered the room without any problems.

Moving into the room properly we made sure all of the techs in the room was standing towards the wall, Maria helped Steve get the computer ready at the same time as me and Sam were making sure the techs were kept in line. "Attention, all S.H.I.E.L.D agents. This is Steve Rogers." Steve started to say, and I could not help but to glance towards him, having a strong feeling what was about to happen. "You've heard a lot about me over the last few days, some of you were even ordered to hunt me down. But I think it is time you know the truth. S.H.I.E.L.D is not what we thought it was, it's been taken over by HYDRA. Alexander Pierce is their leader. The STRIKE and Insight crew are HYDRA as well." Steve started to explain, and I turned my eyes back towards the techs once more.

"I don't know how many more, but I know they're in the building. They could be standing right next to you. They almost have what they want: absolute control. They shot Nick Fury and it won't end there. If you launch those Helicarriers today, HYDRA will be able to kill anyone that stands in their way, unless we stop them. I know I'm asking a lot, but the price of freedom is high, it always has been, and it's a price I'm willing to pay. And if I'm the only one, then so be it. But I'm willing to bet I'm not." Steve finished, and taking that as a hint Sam and I knocked the techs out.

"Did you write that down first, or was it off the top of your head?" Sam asked, and I could not help but to smile. "Oh, he wings it." I answered, and Steve just looked at me with narrowed eyes. "But now is not the time, Maria you take it from here. We need to take down dose Helicarriers once and for all." I then told them. Maria nodded her head and sat down at computer, sending her one last look I left the room with Sam and Steve after me. "Just one question, how do we know the good guys from the bad guys?" Sam asked as we left the building. "If they're shooting at you, they're bad." Steve answered him, and I just shook my head. "See you on the other side." I told the two of them before taking off towards the Helicarrier that I was going to take down. "Until we meet again!" Sam called back before he flied of.

Running towards the Helicarrier I quickly, somehow managed to sneak onboard before they closed of the hangar. "Hey guys, I have found those bad guys you we were talking about." I could hear Sam saying over the com system and I just rolled my eyes over it. "You okay?" Steve asked, it was being clear that he was in a middle of a fight. "I'm not dead yet." Sam answered that. "Guys, keep your heads in the game." I told them, slowly moving away from my hiding spot. "And how did you guys managed to get into this much trouble in such a short time?" I then asked them, looking around myself as I moved. Both happy and worried that there were no agents to be seen.

Moving upwards I made sure to keep to the shadows, feeling for different vibrations as I moved just to make sure that I was alone. Finally reaching my destination I could not let go of the feeling that something was very wrong, only to shake that feeling away from the time being. Opening the hatch I could see the controls and smiled. "Quake in location." I told Maria, Sam and Steve through the com system. "Good job Quake. Falcon, status?" Maria answered, and I smiled. "Engaging." Was the answer we got back from Sam.

"Alright, I'm in." He then said a few seconds later, and I could feel a little bit of my worry die down. "SHIT!" I then could hear Sam saying and I tensed up once more. "Eight minutes, Cap!" Maria asked, feeling like she had not even heard Sam in the first place. "Working on it." Steve answered us. "Alpha locked." Steven then told us, and I let out a sigh of relief. "Falcon?" Maria asked, and I was getting ready. "I had to take a detour!" Sam answered us all and I looked towards the side where I knew Sam would be working. "I'm in. Bravo locked!" Sam finally told us, and I quickly got to work. Carefully taking out the chip that was in I put in the one that would put all of this to an end. "Echo Locked!" I told them once was done, letting out a deep breath of relief. "Good work guys!" Maria told us, and I smiled once more.

"Hello Daisy." A voice suddenly said behind me and I froze up when I heard who it was. "Oh shit!" I said to myself and slowly turned around. "Daisy what's wrong?" I could hear Maria asking. However, I only ignored her as my eyes landed on the last person I thought I would see. "Daisy! Report back, that's an order!" I could hear Maria call out once more. However, I turned the com off. "How did you get out!" I demanded, my eyes narrowed as I looked at a smiling Grant Ward.

"Oh, I was let out of course. Garret on the other hand did not have the same luck on that point. I guess the STRIKE team liked me more." Ward told me, and he slowly walked towards me. Taking my stand, I made sure it was only us here. "You know, that punch you through really hurt." Ward told me as he took yet another step forward. "Not to mention you managed to full us all with that mask of yours. I see know that you have finally dropped it, you know. Your father went through a lot of work into trying to find you too." Ward contained, and I tried to stay as calm as possible.

"Well, what can I say. I was trained by the best." I told him, lifting my arms I made sure he went flying. He hit the wall hard, lowering my arms I hoped that this would have knocked him out. However, when Ward started to move once more I bit myself in the lip and took a deep breath. "So, he was saying the truth, you are a power individual." Ward pointed out and for some reason I could not help but to roll my eyes at that. "And it seems like you didn't learn to stay down when you get knocked down." I told him, my eyes narrowed.

I could see how Ward was coming towards me in full speed, taking a quick step to the side he missed me by a few millimeters. As Ward was stumbling a bit forward I took my chance, with all the power I could managed to gather in such a short distant, I kneed Ward as hard as possible in his stomach. When he bowed down a bit do to the sudden pain I lift my right arm up before forcing it down once more, my elbow hitting Ward right between his shoulder blades. Smiling at my victory I didn't see his next move before it was too late and I found myself falling head first towards the floor. I could hear the small sound of my nose breaking, not badly enough to make me scream out in pain but enough to make it bleed.

Lifting myself up a bit I whipped away the blood and my eyes narrowed at the sight. "Wrong move robot." I growled up as I stood up, turning around I could see a grin on his face. I quickly sent Ward flying the air with another shock wave and before he could get up this time I made sure he had enough ICER bullet in him to make him a sleeping beauty. Whipping away more blood I took a deep breath and started to find my way down once more, knowing that what happened here today was something I could not tell anyone. Now wasn't the time to seek out revenge, it was time to rebuilt something that was once an amazing idea. We now had a chance to build up S.H.I.E.L.D the way it was supposed to be.

It was time to create the organization that Peggy Carter and Howard Stark would be proud over.


	6. Beginning of the end

**_AN: Hello all, Ryuu here with some information. First off, sorry for the long wait on a chapter. Both my life and my beta reader life has been very hectic. Hopfully things will soon fall into place once more. Second off... this is the last chapter of Deep Shadow Condition, but dont worry. I have already finished writing 10 chapter for the next part so its on its way! Now I wont keep your time, lets see how this all ends._**

 _All rights goes to Marvel!_

 _Daisy Johnson POV_

Tapping my foot, I waited for the door to open at the same time as I kept an eye around myself. Hearing the elevator opening further down the corridor just made me pull my hood down, just to cover up my face even more. As the person walked passed me the door opened and my eyes landed on the woman that was standing in front of me. Her brown hair was a mess and she was holding her night robe together. "What?" She asked, it being clear that I had woken her up and I could not help but to smile a little. "I'm sorry Darc, I didn't mean to wake you up." I told Darcy, keeping my voice low as I spoke. Darcy blinked a little in confusion before she lowers herself down a bit to look under my hood.

Giving Darcy a smile I could see how her eyes grow in surprised and before I knew it I was pulled into the room. "What gives Dee!" Darcy asked the moment the door closed behind me. "You need to be more specific Darc." I told her, lifting my hands up to move my hood down. "I mean what were…" Darcy started to say only to stop when she got a look at me. "Sit down!" Darcy told me, pointing towards the couch before she headed of towards the bathroom. Rolling my eyes, I did as I was ordered and sat down.

Darcy emerge from the bathroom a few seconds later, her hair was pulled into a low pony tail, her glasses were on and she was holding on to a first aid bag. "How did you even end up with that?" She asked, putting down the bag in the progress and opened it. "I run into Ward." I told her before I had a chance to stop myself. "Ward? The traitor? The one that you put in jail because of the HYDRA part?" Darcy asked, and I nodded my head. "The HYDRA agents within S.H.I.E.L.D let him out. He tripped me, and I feel head first to the floor." I explained, and Darcy started to look over my nose.

"I managed to check it out earlier, it's no big deal. It's not broken but it hurts, and I can't really walk right into a drug store at the moment. I'm supposed to keep a low profile." I explained, and Darcy lifted one eyebrow as she looked at me. "And you came here?" She asked, there was a hint of laughter in her voice as she spoke. "Well, I don't have that many friends that I trust with my life." I pointed out and Darcy waved her finger toward me. "So, what you just came here for the drugs then." Darcy joked, and I let out a deep sigh. Darcy winked before she headed for the kitchen, returning a few minutes later with a glass of water that she handed over.

"You are leaving as soon as the drug kicks in, aren't you?" Darcy then asked, and I nod my head. "Well, I would hope that you at least wait until nightfall. Easier to sneak out then, right into the shadows of the night." She told me, and I nodded my head. "Fine, I guess I could stay until nightfall." I agreed with her and leaned back in the couch and Darcy sat down beside me. "So, what is the plan now?" She asked, and I took a deep breath. "I ordered the others that once we were done they should go into hiding, to stay low. I will contact them within a week about where we will meet up. If they want to that is." I explained, and Darcy nods her head.

"I also guess that you told them no contact during this time?" She then asked, now it was my time to nod my head. "However, you know exactly what has happened to everyone." Darcy pointed out and I could not help but to smile a little. "Well, almost everyone." I corrected her, and Darcy rolled her eyes. "Anything to worry about?" She asked, and I looked at her with one eyebrow up. "Do you think I would be sitting here if something was very wrong?" I asked, and Darcy shrugs. "Who knows, so much has happened this past year." She pointed out and I could do nothing but to smile at that.

"Which reminds me, I didn't only come here for the drugs." I told her, and Darcy looked a bit sceptic at that. "Oh yeah?" She asked, and I rolled my eyes. "No, I'm here to hand over this." I told her as I pulled out a piece of paper from my jacket. "The contact info to one of the lawyer Stark has. If you, Jane or anyone else that has been around the Avengers were to be questioned on anything now that all of S.H.I.E.L.D's secrets are out, all you need to do is to contact that lawyer and everything will be taken care off." I explained, and Darcy took the paper. "Handy trick." She pointed out when she read through the contact info. "I was going to meet Jane today but…" She then started to say, only to stop when I lift my hand. "No, go and meet her. It would look suspicious otherwise. I'll just crash here on the couch for the time being." I told her, putting my legs over hers in the progress. "Fine, just don't do anything stupide when I'm gone. You know I love to help out if you do." Darcy told me, I moved my leg a little as she tried to get up.

"Oh Darcy, Darcy, Darcy. You know better than anyone that I can't make a promise like that." I answered in a low voice, just as Darcy left the apartment.

 _-X-X-X-X-X-X-X-X-_

 _A week later:_

"Alright then. Anybody asks for me, tell them they can find me right here." I could hear Fury saying, making me stop behind one of the big trees at the graveyard. Carefully looking around the tree I could see how Fury sends one last look towards his own gravestone before walking off. As I was about to walk forward I could see Natasha walking towards Steve and Sam from the other direction. Deciding to stay put for the moment, I leaned towards the tree trunk to listen. "You should be honoured, that's as close as he gets to saying thank you." I could hear Natasha explain and I could not help but to smile at that.

"Not going with him?" Steve asked, and I could hear he was a bit surprised over that. "No." Natasha answered shortly. "Not staying here?" Steve asked once more, and I could almost see the frustration on his face. It was clear that Natasha was playing him once more. "I blew all my covers, I got to figure out a new one." Natasha finally answered, and I took that as my cue to leave my hiding spot. "That might take a while." I could hear Steve point out and I saw how Natasha nods her head at that. "I'm counting on it." She answered him after that. "It doesn't have to take time." I told her, making the three jump a bit as neither of them had seen or heard me coming. "I have a few covers that was never within a database. Besides, I the perfect place to work from." I continued to tell them, only to have my eyes land on the file that Natasha was holding onto.

"However, it seems like someone might not follow with us." I then added, and I could see confusion on both Steve and Sam's faces, Natasha only smiled at that and she holds up the file to Steve. "That thing you asked for, I called in a few favours from Kiev." She explained as Steve took hold of the file that said file no. 17. "Will you do me a favour?" She then asked, walking between both Sam and Steve so that she come to stand beside me. "Call that nurse." She then added and looked back at Steve. "She's not a nurse." Steve told her, and I could not help but to roll my eyes and cross my arms, knowing full well who Natasha was trying to set Steve up with.

"And you are not a S.H.I.E.L.D agent." Natasha pointed out and Steve rolled his eyes, finally giving up. "What was her name again?" He asked, and Natasha smiles big at that. "Sharon. She's nice." She told him, turning her head towards me I nodded it before the two of us turned around. "Be careful, Steve. You might not want to pull on that thread." Natasha called back to them and I turned my head to the side to give the two boys one last look. "Give me a signal once you give up and I'll give you the location of where we are!" I added with a smile. With that Natasha and I head towards the entrance to the graveyard, a simple grey car was parked right at the gate and with a nod of Natasha's head we entered the car. It was time to meet up with the rest of the family.


End file.
